+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10883 | ||||||||||||
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Title | HSPD1 single ring deposited by spraying (6 ms delay) | ||||||||||||
Map data | unsharpened final map | ||||||||||||
Sample |
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Function / homology | Function and homology information coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell ...coated vesicle / isotype switching to IgG isotypes / mitochondrial unfolded protein response / lipopolysaccharide receptor complex / apolipoprotein A-I binding / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / protein import into mitochondrial intermembrane space / migrasome / high-density lipoprotein particle binding / positive regulation of T cell mediated immune response to tumor cell / Mitochondrial protein import / chaperonin ATPase / positive regulation of macrophage activation / cellular response to interleukin-7 / biological process involved in interaction with symbiont / MyD88-dependent toll-like receptor signaling pathway / 'de novo' protein folding / sperm plasma membrane / B cell activation / B cell proliferation / DNA replication origin binding / apoptotic mitochondrial changes / positive regulation of interferon-alpha production / apolipoprotein binding / positive regulation of interleukin-10 production / protein maturation / response to unfolded protein / chaperone-mediated protein complex assembly / clathrin-coated pit / isomerase activity / sperm midpiece / response to cold / positive regulation of interleukin-12 production / T cell activation / secretory granule / lipopolysaccharide binding / ATP-dependent protein folding chaperone / positive regulation of interleukin-6 production / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of T cell activation / unfolded protein binding / positive regulation of type II interferon production / p53 binding / double-stranded RNA binding / protein folding / single-stranded DNA binding / protein-folding chaperone binding / protein refolding / mitochondrial inner membrane / protein stabilization / early endosome / mitochondrial matrix / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.0 Å | ||||||||||||
Authors | Klebl DP / Gravett MSC / Darrow M / Thompson RF / Muench SP | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Structure / Year: 2020 Title: Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales. Authors: David P Klebl / Molly S C Gravett / Dimitrios Kontziampasis / David J Wright / Robin S Bon / Diana C F Monteiro / Martin Trebbin / Frank Sobott / Howard D White / Michele C Darrow / Rebecca ...Authors: David P Klebl / Molly S C Gravett / Dimitrios Kontziampasis / David J Wright / Robin S Bon / Diana C F Monteiro / Martin Trebbin / Frank Sobott / Howard D White / Michele C Darrow / Rebecca F Thompson / Stephen P Muench / Abstract: A host of new technologies are under development to improve the quality and reproducibility of cryoelectron microscopy (cryoEM) grid preparation. Here we have systematically investigated the ...A host of new technologies are under development to improve the quality and reproducibility of cryoelectron microscopy (cryoEM) grid preparation. Here we have systematically investigated the preparation of three macromolecular complexes using three different vitrification devices (Vitrobot, chameleon, and a time-resolved cryoEM device) on various timescales, including grids made within 6 ms (the fastest reported to date), to interrogate particle behavior at the air-water interface for different timepoints. Results demonstrate that different macromolecular complexes can respond to the thin-film environment formed during cryoEM sample preparation in highly variable ways, shedding light on why cryoEM sample preparation can be difficult to optimize. We demonstrate that reducing time between sample application and vitrification is just one tool to improve cryoEM grid quality, but that it is unlikely to be a generic "silver bullet" for improving the quality of every cryoEM sample preparation. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10883.map.gz | 6.6 MB | EMDB map data format | |
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Header (meta data) | emd-10883-v30.xml emd-10883.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10883_fsc.xml | 4.5 KB | Display | FSC data file |
Images | emd_10883.png | 75 KB | ||
Masks | emd_10883_msk_1.map | 7.3 MB | Mask map | |
Others | emd_10883_half_map_1.map.gz emd_10883_half_map_2.map.gz | 5.4 MB 5.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10883 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10883.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened final map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10883_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10883_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10883_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human mitochondrial 60 kDa heat shock protein (mature)
Entire | Name: human mitochondrial 60 kDa heat shock protein (mature) |
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Components |
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-Supramolecule #1: human mitochondrial 60 kDa heat shock protein (mature)
Supramolecule | Name: human mitochondrial 60 kDa heat shock protein (mature) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: human mitochondrial 60 kDa heat shock protein (mature)
Macromolecule | Name: human mitochondrial 60 kDa heat shock protein (mature) type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SNAAKDVKFG ADARALMLQG VDLLADAVAV TMGPKGRTVI IEQSWGSPKV TKDGVTVAKS IDLKDKYKNI GAKLVQDVAN NTNEEAGDGT TTATVLARSI AKEGFEKISK GANPVEIRRG VMLAVDAVIA ELKKQSKPVT TPEEIAQVAT ISANGDKEIG NIISDAMKKV ...String: SNAAKDVKFG ADARALMLQG VDLLADAVAV TMGPKGRTVI IEQSWGSPKV TKDGVTVAKS IDLKDKYKNI GAKLVQDVAN NTNEEAGDGT TTATVLARSI AKEGFEKISK GANPVEIRRG VMLAVDAVIA ELKKQSKPVT TPEEIAQVAT ISANGDKEIG NIISDAMKKV GRKGVITVKD GKTLNDELEI IEGMKFDRGY ISPYFINTSK GQKCEFQDAY VLLSEKKISS IQSIVPALEI ANAHRKPLVI IAEDVDGEAL STLVLNRLKV GLQVVAVKAP GFGDNRKNQL KDMAIATGGA VFGEEGLTLN LEDVQPHDLG KVGEVIVTKD DAMLLKGKGD KAQIEKRIQE IIEQLDVTTS EYEKEKLNER LAKLSDGVAV LKVGGTSDVE VNEKKDRVTD ALNATRAAVE EGIVLGGGCA LLRCIPALDS LTPANEDQKI GIEIIKRTLK IPAMTIAKNA GVEGSLIVEK IMQSSSEVGY DAMAGDFVNM VEKGIIDPTK VVRTALLDAA GVASLLTTAE VVVTEIPKEE KDPGMGAMGG MGGGMGGGMF |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293 K / Instrument: HOMEMADE PLUNGER Details: the sample was sprayed using a microfludic nozzle, resulting in a delay of 6ms between spraying and freezing. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.5 sec. / Average electron dose: 81.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |